Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:18 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 889/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.7.2 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GRaNIE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GRaNIE |
Version: 1.7.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.7.2.tar.gz |
StartedAt: 2024-03-02 04:54:36 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 05:10:51 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 975.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.7.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GRaNIE’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .performIHW: no visible binding for global variable 'adj_pvalue' Undefined global functions or variables: adj_pvalue * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateStatsSummary 13.538 0.271 17.268 plotDiagnosticPlots_peakGene 9.334 0.208 11.808 addSNPData 8.823 0.462 19.651 addConnections_TF_peak 6.904 1.269 10.936 plotCommunitiesEnrichment 7.300 0.217 9.055 plotDiagnosticPlots_TFPeaks 6.425 0.151 8.202 plotGeneralGraphStats 5.839 0.094 7.425 plotPCA_all 5.588 0.215 7.112 calculateCommunitiesEnrichment 5.617 0.166 7.027 plotCommunitiesStats 5.338 0.158 6.844 visualizeGRN 5.092 0.153 6.495 plotCorrelations 4.983 0.127 6.228 plotTFEnrichment 4.731 0.119 6.056 plot_stats_connectionSummary 4.142 0.106 5.361 addConnections_peak_gene 4.045 0.115 6.063 getGRNSummary 4.031 0.105 5.178 getParameters 3.921 0.105 5.043 changeOutputDirectory 3.925 0.096 5.235 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GRaNIE’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GRaNIE)
GRaNIE.Rcheck/GRaNIE-Ex.timings
name | user | system | elapsed | |
AR_classification_wrapper | 0.001 | 0.001 | 0.001 | |
addConnections_TF_peak | 6.904 | 1.269 | 10.936 | |
addConnections_peak_gene | 4.045 | 0.115 | 6.063 | |
addData | 0.000 | 0.001 | 0.001 | |
addSNPData | 8.823 | 0.462 | 19.651 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 2.793 | 0.093 | 3.782 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.858 | 0.095 | 3.845 | |
calculateCommunitiesEnrichment | 5.617 | 0.166 | 7.027 | |
calculateCommunitiesStats | 2.881 | 0.117 | 3.921 | |
calculateGeneralEnrichment | 3.488 | 0.126 | 4.494 | |
calculateTFEnrichment | 3.746 | 0.092 | 4.859 | |
changeOutputDirectory | 3.925 | 0.096 | 5.235 | |
deleteIntermediateData | 2.812 | 0.076 | 3.737 | |
filterConnectionsForPlotting | 2.925 | 0.084 | 3.893 | |
filterData | 3.606 | 0.100 | 4.789 | |
filterGRNAndConnectGenes | 2.886 | 0.079 | 3.864 | |
generateStatsSummary | 13.538 | 0.271 | 17.268 | |
getCounts | 3.060 | 0.084 | 3.984 | |
getGRNConnections | 3.892 | 0.092 | 4.998 | |
getGRNSummary | 4.031 | 0.105 | 5.178 | |
getParameters | 3.921 | 0.105 | 5.043 | |
getTopNodes | 2.965 | 0.069 | 3.919 | |
initializeGRN | 0.038 | 0.003 | 0.054 | |
loadExampleObject | 2.894 | 0.073 | 3.760 | |
nGenes | 2.879 | 0.084 | 3.791 | |
nPeaks | 2.864 | 0.075 | 3.766 | |
nTFs | 2.853 | 0.098 | 4.207 | |
overlapPeaksAndTFBS | 2.904 | 0.084 | 3.914 | |
performAllNetworkAnalyses | 0.001 | 0.000 | 0.000 | |
plotCommunitiesEnrichment | 7.300 | 0.217 | 9.055 | |
plotCommunitiesStats | 5.338 | 0.158 | 6.844 | |
plotCorrelations | 4.983 | 0.127 | 6.228 | |
plotDiagnosticPlots_TFPeaks | 6.425 | 0.151 | 8.202 | |
plotDiagnosticPlots_peakGene | 9.334 | 0.208 | 11.808 | |
plotGeneralEnrichment | 3.728 | 0.091 | 5.000 | |
plotGeneralGraphStats | 5.839 | 0.094 | 7.425 | |
plotPCA_all | 5.588 | 0.215 | 7.112 | |
plotTFEnrichment | 4.731 | 0.119 | 6.056 | |
plot_stats_connectionSummary | 4.142 | 0.106 | 5.361 | |
visualizeGRN | 5.092 | 0.153 | 6.495 | |